Search Packages

maldiamrkit

Comprehensive toolkit for MALDI-TOF mass spectrometry data preprocessing for antimicrobial resistance (AMR) prediction purposes

gnomonicus

Python code to integrate results of tb-pipeline and provide an antibiogram, mutations and variants

respredai

Implementation of the pipeline described in the work "Artificial intelligence model to predict resistances in Gram-negative bloodstream infections" by Bonazzetti et al., npj Digit. Med. 8, 319 (2025)

staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

hamronization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

maldibatchkit

Batch-effect correction methods for MALDI-TOF spectra in clinical AMR prediction workflows

maldideepkit

Catalog of sklearn-compatible deep learning classifiers for MALDI-TOF binned spectra

staphscope-typing-tool

StaphScope is a comprehensive bioinformatics tool for Staphylococcus aureus genomic analysis including MLST typing, spa typing, SCCmec analysis, antimicrobial resistance detection, virulence factors, plasmid profiling, and lineage prediction from whole genome sequencing data. Designed specifically for MRSA research